PXD045792

PXD045792 is an original dataset announced via ProteomeXchange.

Title	Don’t Waste Time – Ensure Success in Your Cross-Linking Mass Spectrometry Experiments Before You Begin.
Description	Cross-linking mass spectrometry (XL-MS) is becoming a more popular tool for researchers to turn towards for studying proteins and their complexes of interest especially in complex samples such as lysates or whole-cells. Studying a targeted proteins in a complex mixture can be difficult as data on other higher abundant proteins may dominate, leaving little information on complexes of interest. Although it is known that cross-linking favours proteins of higher abundances, it is yet unclear what it means to be “abundant” to expect good cross-linking data. In this paper, we show that proteins of interest should be at least in the top 20 % abundance range to expect more than one cross-link found per protein. Furthermore, we show that a classical bottom-up LC-MS/MS experiment and iBAQ analysis can help determine the abundance level of proteins and a simple method to follow their enrichment if necessary. We hope that this guideline can be a starting point for researchers who would like to use XL-MS to study their protein of interest and help ensure a successful cross-linking experiment from the beginning.
HostingRepository	PRIDE
AnnounceDate	2024-02-07
AnnouncementXML	Submission_2024-02-07_09:18:43.377.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lucienne Nouchikian
SpeciesList	scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Neisseria meningitidis serogroup C (strain 8013); NCBI TaxID: 604162;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-28 15:06:14	ID requested
⏵ 1	2024-02-07 09:18:44	announced

10.1021/acs.analchem.3c04682;

Nouchikian L, Fernandez-Martinez D, Renard PY, Sabot C, Dum, é, nil G, Rey M, Chamot-Rooke J, Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin. Anal Chem, 96(6):2506-2513(2024) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: Cross-linking, mass spectrometry, protein abundance, iBAQ

Julia Chamot-Rooke
contact affiliation	Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France.
contact email	julia.chamot-rooke@pasteur.fr
lab head
Lucienne Nouchikian
contact affiliation	Institut Pasteur
contact email	lucienne.nouchikian@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/02/PXD045792

PRIDE project URI

• PRIDE
  1. PXD045792
     1. Label: PRIDE project
     2. Name: Don’t Waste Time – Ensure Success in Your Cross-Linking Mass Spectrometry Experiments Before You Begin.